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Antarctic sea-ice extent, primary productivity and ocean circulation represent interconnected systems that form important components of the global carbon cycle. Subdecadal to centennial-scale variability can influence the characteristics and interactions of these systems, but observational records are too short to evaluate the impacts of this variability over longer timescales. Here, we use a 170-m-long sediment core collected from Integrated Ocean Drilling Program Site U1357B, offshore Adélie Land, East Antarctica to disentangle the impacts of sea ice and subdecadal climate variability on phytoplankton bloom frequency over the last ~11,400 years. We apply X-ray computed tomography, Ice Proxy for the Southern Ocean with 25 carbon atoms, diatom, physical property and geochemical analyses to the core, which contains an annually resolved, continuously laminated archive of phytoplankton bloom events. Bloom events occurred annually to biennially through most of the Holocene, but became less frequent (~2–7 years) at ~4.5 ka when coastal sea ice intensified. We propose that coastal sea-ice intensification subdued annual sea-ice break-out, causing an increased sensitivity of sea-ice dynamics to subdecadal climate modes, leading to a subdecadal frequency of bloom events. Our data suggest that projected loss of coastal sea ice will impact the influence of subdecadal variability on Antarctic margin primary productivity, altering food webs and carbon-cycling processes at seasonal timescales., This research used samples and data provided by IODP expedition 318, sponsored by the US National Science Foundation (NSF) and participating countries under the management of the Consortium for Ocean Leadership, including the Australian and New Zealand International Ocean Discovery Program Consortium. Funding was provided by Royal Society Te Apārangi Marsden Fund (18-VUW-089 to R.M.M. and 15-VUW-131 to N.A.N.B.) and the New Zealand Ministry of Business, Innovation and Employment through the Antarctic Science Platform (ANTA1801). Funding was also provided by the New Zealand Ministry of Business, Innovation and Employment Strategic Science Investment Fund (SSIF) through GNS Science (grant 540GCT32). We acknowledge funding from the Dumont d’Urville NZ-France Science and Technology Programme, MARICE project (Marine and Ice core reconstruction of East Antarctic sea ice variability over the past 2,000 years) (project nos. 45455NF and 19-VUW-047-DDU Catalyst Fund, RSNZ). J.E. and X.C. acknowledge funding by the ERC StG ICEPROXY (203441), the ANR CLIMICE and the FP7 Past4Future (243908) projects. F.J.J.-E. was funded by project 201830I092 (Spanish Research Council). C.E. and F.J.J.-E acknowledge funding by the Spanish Ministry of Science and Innovation (grant CTM2017-89711-C2-1-P), co-funded by the European Union through FEDER funds. C.R.R. was funded by a University of Otago research grant and a L’Oréal-UNESCO For Women in Science Australia and New Zealand Fellowship. The Natural Environment Research Council funded K.E.A. (CENTA PhD; NE/L002493/1) and J.B. (standard grant Ne/I00646X/1). Y.Y. was funded by the Japan Society for Promotion of Science (JSPS) grant no. JP20H00193. S.F.P. was supported by National Science Foundation grant OPP-0732796. R.B.D. was supported by National Science Foundation grants PLR-1644118 and OCE-1129101. The authors acknowledge the Norwegian Polar Institute’s Quantarctica package, and the use of imagery from the NASA Worldview application (https://worldview.earthdata.nasa.gov/), part of the NASA Earth Observing System Data and Information System.

Upwelling within the highly productive Benguela current off the Namibian coast began in, and intensified throughout, the Neogene epoch. Model simulations indicate its development was intimately connected to evolving topography and mountain uplift in Africa.